Romanian referee Vlad Iordăchescu was led away by security as ugly scenes marred the end of Belgium's 18-10 win over Spain -- a result that gives the official's countrymen a place at the 2019 Rugby World Cup.
Spain forward Pierre Barthere led the protests at the full-time whistle as aggrieved visiting players attempted to confront the referee.
The visitors felt that a number of decisions had gone against them during a close match, with Iordăchescu's nationality only adding to their frustration.
The Spanish Rugby Federation (FERugby) apologised for the actions of some of its players via Twitter on Sunday evening as it revealed a complaint about the referee's performance would be lodged with Rugby Europe and World Rugby.
"I don't want to think that rugby [has been fixed] to put us out," Spain captain Jaime Nava, who suggested his side had been "eliminated by external factors," told Radio Marca.
"When we were assigned Romanian officials, we were shocked. But this is rugby, the values are assumed."
He added: "The dressing room is down, sunk. For sure, today rugby has lost."
Spain had arrived in Brussels with high hopes of qualifying for next year's World Cup, and needed a victory to secure their place in Japan.
However, defeat means that they must now face Portugal later this year in a playoff for the chance to play Samoa for a place at the quadrennial tournament.
Romania, who have competed in every World Cup since the competition's inaugural edition in 1987, will now advance automatically. The Oaks lost 25-16 in Tbilisi on Sunday but compiled 29 points in qualifying matches across the last two Rugby Europe Championships -- results against Georgia did not count -- three more than Spain.
"I'm the captain and I would like to apologise for what happened with the referee," Nava said. "The image at the end of the game does not represent the sport nor the values of this team. It must be understood however, we've lost part of our dream."
It has not been a good week for official appointments after World Rugby were forced to pull assistant referee Marius van der Westhuizen from England's clash with Ireland on Saturday after he attended a training session with Eddie Jones' hosts.
Although part of the qualification process for the 2019 World Cup, the match in Brussels was part of the 2018 Rugby Europe Championship, and therefore all appointments were made by organisers, Rugby Europe.
World Rugby declined to comment on the situation when contacted by ESPN.